LAUSR

Simple Summary Vesicular stomatitis (VS) is a viral disease that primarily affects cattle, horses and swine. In affected livestock, the VS virus (VSV) causes painful blister-like lesions in the mouth, on the tongue, lips, nostrils, hooves, and teats and infected animals usually refuse to eat and drink, causing livestock production losses. VS is also a zoonotic disease and can cause influenza-like symptoms in humans. In 2018, Ecuador experienced an outbreak of VS affecting cattle in most of the provinces of the country. Here we determined the phylogenetic relationship among the virus strains isolated in that year. Our analysis suggests different transmission patterns in the major geographic regions of Ecuador; several small and independent outbreaks, most probably transmitted by vectors in the Amazon, and an outbreak caused by the movement of livestock and/or fomites in the Andean and Coastal regions. For better control of future outbreaks, we recommend more research into vectors and vertebrate reservoirs in Ecuador. This can further elucidate the mechanisms of the emergence and re-emergence of the virus. Abstract The Vesicular Stomatitis Virus (VSV) is an arbovirus causing vesicular stomatitis (VS) in livestock. There are two serotypes recognized: New Jersey (VSNJV) and Indiana (VSIV). The virus can be transmitted directly by contact or by vectors. In 2018, Ecuador experienced an outbreak of Vesicular Stomatitis (VS) in cattle, caused by VSNJV and VSVIV, with 399 cases reported distributed over 18 provinces. We determined the phylogenetic relationships among 67 strains. For the construction of phylogenetic trees, the viral phosphoprotein gene was sequenced, and trees were constructed based on the Maximum Likelihood method using 2004 outbreak strains from Ecuador (GenBank) and the 2018 sequences (this article). We built a haplotype network for VSNJV to trace the origin of the 2004 and 2018 epizootics through topology and mutation connections. These analyses suggest two different origins, one related to the 2004 outbreak and the other from a transmission source in 2018. Our analysis also suggests different transmission patterns; several small and independent outbreaks, most probably transmitted by vectors in the Amazon, and another outbreak caused by the movement of livestock in the Andean and Coastal regions. We recommend further research into vectors and vertebrate reservoirs in Ecuador to clarify the mechanisms of the reemergence of the virus.